The Molecules of Cells… dun dun dahhhhh – ch 3
Organic chem -
Carbon – most versatile building block – why?
Tetravalence –
Where does the C in your body come from?
Valences of common atoms in orgs
What is the bonding capacity of H?What is the bonding capacity of O?What is the bonding capacity of N?What is the bonding capacity of C?
Which of these would be improperly bonded?
Variation in C skeletons contributes to diversity of organic molecules
Straight, branched, closed rings, some have double bonds, triple
Isomers• molecules w/ same molecular formula (same
number and kinds of atoms) but diff atom arrangements (which atoms are attached to which and how)
Classes of isomers: structural, geometric, enantiomers
Geometric isomers = share same covalent partnerships, but differ in their spatial arrangements.• Result from fact that double bonds will not allow the atoms they join to rotate freely about the axis of the bonds.• Subtle differences affects biological activity.
• Enantiomers = mirror images of each other.• Can occur when 4 diff atoms or groups of atoms are
bonded to the same carbon (asymmetric carbon).• 2 diff spatial arrangements of the four groups around
the asymmetric carbon. These arrangements are mirror images.
• Usually one form is biologically active and its mirror image is not.
How many asymmetric carbons are present?
Functional Groups• contribute to molecular
diversity of life• frequently bonded to
carbon skeleton of organic molecules.
• Have specific chemical and physical properties.
• Are the regions of organic molecules which are commonly chemically reactive.
• Behave consistently from one organic molecule to another.
• Depending upon their number and arrangement, determine unique chemical properties of organic molecules in which they occur.
Hydroxyl
- OH• polar group• Conveys water solubility • Organic compounds with hydroxyl groups are called
alcohols.
Carbonyl Group-C=O• polar group• Conveys water solubility.• found in sugars.• at the end of skeleton called aldehyde.• at the middle of skeleton called ketone
Carboxyl Group• polar group • Conveys water solubility • Since it donates protons, has acidic properties. • Compounds w/ this group are called carboxylic acids.
Amino Group
• polar group • Conveys water solubility• Acts as weak base. The unshared pair of electrons on
the nitrogen can accept a proton, giving it a +1 charge.• Organic compounds w/ this group are called amines.
Sulfhydryl Group• Help stabilize the structure of proteins. • Organic compounds with this functional group are
called thiols.
What other functional groups do you see in this molecule?
Could this molecule have an enantiomer isomer? How do you know?
Phosphate Group• Loss of two protons leaves phosphate group w/ a -
charge.• Has acid properties since it loses protons.• Polar group • Conveys water solubility• Important in cellular energy storage & transfer
Methyl Group
• Non polar• Conveys hydrophobic properties
Macromolecules, baby!
CarbsLipidsProteinsNucleic acids
Some basics
Polymer – long molecule consisting of many similar or identical building blocks linked by covalent bonds
Monomer -
How do the bonds b/t monomers form?Condensation rx or dehydration synthesis – removal of
water from monomersFacilitated by enzymes – speed up the rx
How do the bonds b/t monomers break?
Hydrolysis – bonds broken by addition of water Hydro = waterLysis = breakEx: digestionEnzymes facilitate
Diversity of macromolecules
26 letters make many words40-50 monomers make many macromoleculesKey is in arrangement of monomers
Tac Act Cat
Carbohydrates • Function – fuel & building mat.• Sugars & their polymers• simplest are monosaccharides or simple sugars.• Disaccharides (double sugars) consist of 2 monosaccharides
joined by condensation reaction.• Polysaccharides - polymers of many monosaccharides.
monosaccharides• some multiple of the unit CH2O.• Ex: glucose = C6H12O6.• Funcitonal groups: carbonyl group (>C=O) and multiple hydroxyl
groups (—OH).• names end in -ose.•
Diversity of monosaccharides• classified by # of carbon atoms in skeleton (3-7)• Some are enantiomers of each other - spatial
arrangement of their parts around asymmetric C atoms.
Structural isomers enantiomers
Monosaccharides cont…• most form rings in aqueous solutions.• major nutrients for cellular work.
Disaccharides• glycosidic linkage to form a disaccharide via
dehydration.• Maltose - joining 2 glucose• Sucros- joining glucose & fructose. • Lactose - joining glucose & galactose.
Polysaccharides - storage• Function in storage & structural roles.• 100s – 1000s of monosaccharides joined• Starch - plant storage polysac composed entirely of glucose
monomers.• Plants store surplus glucose as starch granules within plastids,
including chloroplasts & withdraw as needed for E or C.• Glycogen – animal storage polysac. Store 1 day supply in liver
& muscles
Polysaccharides - structural• Cellulose – plant structural polysac - major component of cell walls
– most abundant organic compound on Earth.– Like starch, cellulose is polymer of glucose. However, the glycosidic
linkages in these two polymers differ.– Digestion... Symbiotic orgs
• Chitin – animal structural polysac - found in the exoskeletons of arthropods– also provides structural support for cell walls of fungi.
Lipids• Consist mostly of hydrocarbon• Little – no affinity for H2O (water insoluble)• Not polymers• 3 families
– Fats– Phospholipids– Steroids
Fats• Glycerol & & fatty acid• Dehydration synthesis• Linkage – ester• Vary in length & the # & location of double bonds• Functions:
– E storage– Cushions organs– Insulates body
2 main types of fats1. Saturated – saturated w/ H; no double bonds
– Animal fats– Solid @ room temp… why?– Contribute to arteriosclerosis
Yum!
2 main types of fats2. Unsaturated – not saturated w/ H; has double bonds
Creates kink in shape @ double bondLiquid @ room tempPlants & fishPeanut butter? Why solid?
Phospholipids• 1 glycerol• 2 fatty acids• 1 phosphate group
Phospholipids
• Amphipathic• Major component of cell membranes• Structure determines function
Steroids
• C skeleton consisting of 4 interconnected rings.• Vary based on functional groups• Cholesterol – imp. In membranes of animal cells
– Most other steroids made from it
Proteins!• large • funcitons:
– Structure (silk)– Storage (casein)– Movement (actin &
myosin)– Defense (antibodies)– Regulation of metabolism
(enzymes)– Transport (hemoglobin)– Communication
(hormones)– receptor proteins
basics• Monomer –
amino acids (20 diff)– Vary based on
R groups– Structure of aa– Linkage –
peptide bond– Backbone– Aka
polypeptide
Condensation reaction or dehydration synthesis
Conformation = 3 D shape of a protein molecule
Shape determines functionDNA codes for the type of aa & what order they’re
bonded in So…
DNA codes for which proteins you make & which proteins you make determines your physical characteristics
Proteins are so complex that we
describe their structure on 4
levels
1. Primary structure• the seq of aa• Det by DNA• Sanger, insulin
Notice primary structure & backbone
Proteins are so complex that we
describe their structure on 4 levels
2) Secondary structure• Pattern of folds &
coils that result from the H-bonding at regular intervals along the polypeptide backbone.
• 2 types: alpha helix & pleated sheet
Proteins are so complex that we
describe their structure on 4 levels
3) Tertiary structure• Irregular contortions
that result from bonding b/t R groups of the aa
• Types of bonds that can occur b/t R groups:– H-bonds, disulfide
bridges, ionic, hydrophobic interactions
Proteins are so complex that we
describe their structure on 4
levels
4) Quaternary structure
• Only those composed of 2 or more polypeptide chains
• Overall structure that results from the aggregation of polypeptide chains
Emergent property?
Specific function of a protein arises from the architecture of the molecule
Denaturation?• Loss of conformation of a protein• Causes? High temps, change in salt concentration,
change in pH
Review of levels
•Deoxyribonucleic acid (DNA) & RNA•Double helix•Watson and Crick—1953•Made of smaller molecules called nucleotides bonded together
Nucleic Acids
Relationship between DNA & chromosomes?
Chromosomes are made of DNA!
Monomers are nucleotides
5 Different ones • Deoxyribose: sugar molecule• Phospahte group: a phosphorus atom surrounded by oxygen• Nitrogen containing base: molecule containing nitrogen
adenine (A)guanine (G)cytosine (C)thymine (T)
Dehydration synthesis & then H-bonds b/t N bases
Complementary Base Pairing
• Cytosine - Guanine• Adenine - Thymine• Connected by H-bonds• Allows DNA to make exact
copies of itself
DNA REPLICATION
http://www.lewport.wnyric.org/jwanamaker/animations/DNA%20Replication%20-%20long%20.html
Complementary Base Pairs
• TTACGGCAT base pair would be????
DNA & RNA
DNA & RNA Compared
DNA RNA
Sugar deoxyribose ribose
Strands double single
Bases A,G,C,T A,G,C,U
(uracil)
Notice the difference between
the 2 sugars?
Sugar in DNA
Sugar in RNA
How is DNA the code for life?• Gene – portion of DNA that codes for the making
of polypeptide (protein) • What makes you unique is all the particular
proteins you make.